Methods and systems for cell and bead processing

Abstract

The present disclosure provides methods and systems for cell and bead processing or analysis. A method for processing a cell or bead may include subjecting a bead to conditions sufficient to change a first characteristic or set of characteristics (e.g., cell or bead size). Such a method may further include subjecting the cell or bead to conditions sufficient to change a second characteristic or set of characteristics. In some cases, crosslinks may be formed within the cell or bead.

What is claimed is: 
     
       1. A method of processing a cell, comprising:
 (a) contacting said cell with a first chemical species and a second chemical species, wherein said first chemical species is capable of changing a cross-section of said cell from a first cross-section to a second cross-section, which second cross-section is less than said first cross-section, and wherein said second chemical species is capable of forming crosslinks within said cell, thereby generating a fixed cell having said second cross-section; 
 (b) providing said fixed cell having said second cross-section in an aqueous fluid; 
 (c) partitioning said fixed cell having said second cross-section into a partition; and 
 (d) lysing said fixed cell having said second cross-section in said partition. 
 
     
     
       2. The method of  claim 1 , wherein said crosslinks are formed upon cross-linking one or more cross-linkable molecules within said cell. 
     
     
       3. The method of  claim 2 , wherein said one or more cross-linkable molecules are one or more polymers. 
     
     
       4. The method of  claim 1 , wherein said crosslinks are formed upon polymerizing a plurality of monomers within said cell. 
     
     
       5. The method of  claim 1 , wherein said cross-section of said cell is changed from said first cross-section to said second cross-section concurrently with formation of said crosslinks within said cell. 
     
     
       6. The method of  claim 1 , wherein said crosslinks are formed subsequent to changing said cross-section from said first cross-section to said second cross-section. 
     
     
       7. The method of  claim 1 , wherein said second cross-section is substantially maintained in said aqueous fluid. 
     
     
       8. The method of  claim 1 , wherein said partition is a droplet. 
     
     
       9. The method of  claim 8 , wherein a volume of said droplet is less than 10,000 pL. 
     
     
       10. The method of  claim 1 , wherein said second chemical species is selected from the group consisting of disuccinimidyl suberate (DSS), dimethylsuberimidate (DMS), formalin, dimethyladipimidate (DMA), dithio-bis(-succinimidyl propionate) (DSP), disuccinimidyl tartrate (DST), and ethylene glycol bis(succinimidyl succinate) (EGS). 
     
     
       11. The method of  claim 1 , wherein said first or said second chemical species is selected from the group consisting of an organic solvent and a cross-linking agent. 
     
     
       12. The method of  claim 11 , wherein said organic solvent is acetone or an alcohol. 
     
     
       13. The method of  claim 11 , wherein said cross-linking agent is selected from the group consisting of a photocleavable crosslinker and an aldehyde. 
     
     
       14. The method of  claim 1 , further comprising providing said cell in an aqueous reaction mixture, wherein said cell comprises a target molecule, and performing one or more reactions using said target molecule. 
     
     
       15. The method of  claim 14 , further comprising performing said one or more reactions in said partition. 
     
     
       16. The method of  claim 15 , wherein said partition is a droplet or a well. 
     
     
       17. The method of  claim 15 , wherein said target molecule is a nucleic acid molecule and wherein said partition further comprises a plurality of nucleic acid barcode molecules, wherein each nucleic acid barcode molecule of the plurality of nucleic acid barcode molecules comprises a sequence comprising a common barcode sequence. 
     
     
       18. The method of  claim 17 , wherein said plurality of nucleic acid barcode molecules are attached to a bead. 
     
     
       19. The method of  claim 18 , wherein said plurality of nucleic acid barcode molecules are releasably attached to a bead, and the method further comprises releasing said sequences of said plurality of nucleic acid barcode molecules from said bead within said partition. 
     
     
       20. The method of  claim 18 , wherein said bead is a gel bead. 
     
     
       21. The method of  claim 20 , wherein said gel bead is degradable upon application of a stimulus. 
     
     
       22. The method of  claim 1 , wherein said cross-section is a diameter or a volume of said cell. 
     
     
       23. The method of  claim 1 , wherein said second cross-section of said cell is reduced by at least 5% compared to said first cross-section. 
     
     
       24. The method of  claim 1 , wherein said change from said first cross-section of said cell to said second cross-section is irreversible. 
     
     
       25. The method of  claim 1 , wherein said changing said cross-section of said cell from said first cross-section to said second cross-section is reversible upon application of a stimulus. 
     
     
       26. The method of  claim 25 , further comprising applying said stimulus, wherein application of said stimulus reverses said change from said first cross-section to said second cross-section by at least 75%. 
     
     
       27. The method of  claim 1 , wherein said contacting said cell comprises contacting said cell with said first chemical species and said second chemical species at a same time. 
     
     
       28. The method of  claim 1 , wherein said contacting said cell comprises contacting said cell with said first chemical species and said second chemical species at a different time. 
     
     
       29. A method of processing a cell, comprising:
 (a) subjecting said cell to conditions sufficient to:
 (i) change a cross-section of said cell from a first cross-section to a second cross-section, which second cross-section is less than said first cross-section, and 
 (ii) form crosslinks within said cell having said second cross-section, thereby generating a fixed cell having said second cross-section; 
 
 (b) providing said fixed cell having said second cross-section in an aqueous fluid; 
 (c) partitioning said fixed cell having said second cross-section into a partition; and 
 (d) lysing said fixed cell having said second cross-section in said partition.